I need to replace my existing furnace where the cold air return fits into the rear of the furnace. The repairman that came out told me that new furnaces don't allow rear cold air return because of the location of the blower and that it would be an extra $1000 to run the cold air return under the new furnace.
Is this actually the case or are there new furnaces that wouldn't require all this extra work?

Since I'm not an hvac guy, maybe get a couple additional quotes. Talk to the companies on the phone to explain your situation first and see what they say about their ability to work with your situation.
just my .o2, Doug

Welcome PepperGang:
I'm more than a little leary of the serviceman's statement. It would be necessary to cut the back out of the furnace, of course and that would be a hard cut but I haven't met a blower that has any idea where the air is coming from.
The thousand dollar duct under the furnace is a nice round, terrorizing number that says "back off". The furnace is typically much shorter than the older ones, so why not raise the furnace up, put a plenum under it and cut the return in the plenum. A universal plenum would cost maybe, $30 and just slips togather; how much is that worth?
Glenn

I'm in contract for my first house right now, and had my inspection yesterday. When I opened the cabinet with the heater, I saw everything connected as normal, except for a flexible 5" pipe just dangling from the ceiling in the heater closet. I asked the inspector what that was for, and he said it was the cold air return, just venting into the same space as the heater. He said it went to the roof, and brought fresh air into the chamber, for the heater to use. It wasn't connected to anything, just a vent line to the outside, and it worked just fine.